I don't think it was all bad at all. While it's the most flawed of the main trilogy to be sure, I still think it does more good than bad, and I think what it does right, it even does better than the Singer films (that said, the Singer films obviously excel in areas that X-Men: The Last Stand doesn't) For my list:

Beast
Beast was a great addition to the franchise. I felt he was portrayed perfectly from the comics. He's one of the better characters in the entire series off this one movie alone (X-Men: First Class certainly helped that, but X-Men: The Last Stand was the better portrayal of Beast). I even like how Beast is a former student who is returning to the team in a time of need, a nod to the actual Dark Phoenix Saga where Beast is a former X-Man that returns to the team. I don't know if that little nod was intentional or unintentional, but I liked it.

Dark Phoenix Saga
I know this is what gets the most **** about the movie, but I thought it was an interesting take on the character (I prefer split personalities over space entity - I think it's more realistic and believable, and also still gets the same point across), and most of the elements of the film version can be found in the comics. Xavier's psychic blocks are an element in the comics, Logan struggling with killing Jean, hell, even the killing of Cyclops at least ties itself to the comic book motivations. While the comics have Cyclops as the one person Jean can't / won't kill due to their connection, their bond, it is watching Cyclops struck down in the final battle that finally drives Jean past all the mental blocks and Phoenix comes back once more. In the movie, Phoenix kills Cyclops, and it is this that drives Jean's motivations of running, and eventually, wanting to die. Cyclops still drives her entire motivation, so while I don't like killing off Cyclops, it at least is still the driving factor of her motivation. The explanation of Phoenix being a creature of pure desire, joy, and rage, as Xavier explains to Logan, fits in with the Dark Phoenix Saga, as through Jean, Phoenix is able to experience emotions of joy and pleasure that it never experienced before, and it's not willing to give those up. The movie version of the Dark Phoenix Saga checks all the same boxes as the comic version, it just does it in different ways.

The Cure
While a lot of people also had problems with the movie focusing on 2 plot lines, I didn't. Magneto had been building up his war in his mind for 2 movies, and we had to see it. It couldn't just be forgotten about because of Jean. I thought the cure was a good story to use, and I thought that it fit in well as a follow up to X-Men and X2, as well as a good plot to run parallel with The Phoenix Saga. It allowed us to finally see Magneto and the Brotherhood go all out as mutant terrorists, something Singer's films didn't really do, as well as finally give cause for Magneto to bring his war to humanity's doorstep. Magneto was quite possibly at his best of the main trilogy in this film. His 2 speeches were great character moments that were delivered brilliantly by Ian McKellen, and his displays of power were much more aggressive and ruthless.

It was the most comic booky
This one felt, more than X-Men or X2, like it was taken out of the pages of the comics. I do appreciate Singer's films for being so grounded in reality. I felt that was the right direction to take, and I wouldn't want Singer's films re-done any differently. But X-Men: The Last Stand keeps that "grounded in reality" vision, and ups the stakes, giving it a lot more excitement than Singer's 2 films, and a lot more comic book style action, without going too over the top.

In the end, I thought that X-Men: The Last Stand told the best story of the main trilogy (and didn't butcher it as badly as some people feel it did), and was a fitting climax to the ongoing story arcs. I did certainly suffer in some areas - some were continuations of the mistakes that Bryan Singer and co. made, some were brand new mistakes - but all the movies made mistakes, quite frankly, and this one was no different. Like the other movies, I was able to look past the mistakes that it did make, because what it did right well outweighed what it did wrong. And to this day, the finale with Logan marching up to kill Jean is one of my favorite sequences in the entire series.